Registration of nominee

Just make a deed declaring him your heir.  Even you can make a will deed and  register that .

Is it to be done on a stamp paper? Where it can be done? Thank you 

There is no provision in law to make nomination for a shop unless you own the shop as member of a co-operative society. If you are owner as member of a co-operative society, you can file nomination with the society. But courts have held that nomination does not confer absolute ownership on the nominee.  In order to confer absolute ownership you should make a will. The will can be made on plain paper and it is not necessary to register it. But the will should be attested by two witnesses, in whose presence you should sign the will.  After your death the witnesses may be called before the magistrate to confirm that they had seen you sign the will. In Mumbai all wills are subject to probate and probate attracts stamp duty. I do not know whether Nerul is considered Mumbai for this purpose. I suggest you do both nomination and will. Nomination will facilitate hassle free transfer and probate, if necessary, can be applied for in due course of time.

You have not posted complete facts.

As already stated by other Expert, there is no provision for the Nomination of immovable property.

You may execute a Gift Deed in favour of your Nominee and get it registered. Stamp Duty differs from state to state. You may contact the Sub Registrar Office for details of stamp duty. If you do not wish to spend money towards the Stamp Duty on Gift Deed, you may write a Will and get the same registered for which the stamp duty is negligible.